Detailed view for PF3D7_1245400

Basic information

TDR Targets ID: 5490
Plasmodium falciparum, mitochondrial ribosomal protein L3 precursor, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.4292 | Length (AA): 341 | MW (Da): 39766 | Paralog Number: 1

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00297   Ribosomal protein L3

Gene Ontology

Mouse over links to read term descriptions.
GO:0005762   mitochondrial large ribosomal subunit  
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0006412   translation  

Metabolic Pathways

Ribosome (KEGG)

Structural information

Modbase 3D models:

There are 2 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
80 289 4wfa (B) 2 216 27.00 0 1 0.838336 0.91
80 291 5dm6 (B) 1 205 31.00 0 0.97 0.876901 1.11

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile gametocyte, sporozoite, early schizont, early trophozoite, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile merozoite, early ring, late ring, late schizont, Sporozoite, Female Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Ring, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 0 hs. Otto TD
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127133)

Species Accession Gene Product
Arabidopsis thaliana AT3G17465   50S ribosomal protein L3-2
Arabidopsis thaliana AT2G43030   50S ribosomal protein L3-1
Babesia bovis BBOV_III008320   50S ribosomal protein L3, putative
Babesia bovis BBOV_I004730   ribosomal protein L3 domain containing protein
Brugia malayi Bm1_56120   Mitochondrial 39S ribosomal protein L3
Candida albicans CaO19.7485   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPL9 (YGR220C) large subunit protein (E. coli L3)
Caenorhabditis elegans CELE_C26E6.6   Protein MRPS-18C
Chlamydia trachomatis CT_528   50S ribosomal protein L3
Dictyostelium discoideum DDB_G0288983   ribosomal protein L3, mitochondrial
Drosophila melanogaster Dmel_CG8288   mitochondrial ribosomal protein L3
Escherichia coli b3320   50S ribosomal subunit protein L3
Echinococcus granulosus EgrG_000927800   39S ribosomal protein L3 mitochondrial
Echinococcus multilocularis EmuJ_000927800   39S ribosomal protein L3, mitochondrial
Homo sapiens ENSG00000114686   mitochondrial ribosomal protein L3
Leishmania braziliensis LbrM.29.0040   ribosomal protein L3-like protein
Leishmania donovani LdBPK_290030.1   ribosomal protein L3-like protein
Leishmania infantum LinJ.29.0030   ribosomal protein L3-like protein
Leishmania major LmjF.29.0030   ribosomal protein L3-like protein
Leishmania mexicana LmxM.08_29.0030   ribosomal protein L3-like protein
Mycobacterium leprae ML1863c   PROBABLE 50S RIBOSOMAL PROTEIN L3 RPLC
Mus musculus 94062   mitochondrial ribosomal protein L3
Mycobacterium tuberculosis Rv0701   50S ribosomal protein L3 RplC
Mycobacterium ulcerans MUL_0790   50S ribosomal protein L3
Neospora caninum NCLIV_018210   50S ribosomal protein L3, putative
Neospora caninum NCLIV_030720   ribosomal protein L3p, putative
Oryza sativa 4327104   Os01g0251100
Oryza sativa 4328236   Os02g0137200
Plasmodium berghei PBANKA_1458600   mitochondrial ribosomal protein L3 precursor, putative
Plasmodium berghei PBANKA_0819200   50S ribosomal protein L3, apicoplast, putative
Plasmodium falciparum PF3D7_1245400   mitochondrial ribosomal protein L3 precursor, putative
Plasmodium falciparum PF3D7_0918200   50S ribosomal protein L3, apicoplast, putative
Plasmodium knowlesi PKNH_1465100   50S ribosomal protein L3, putative
Plasmodium knowlesi PKNH_0716200   50S ribosomal protein L3, apicoplast, putative
Plasmodium vivax PVX_099330   50S ribosomal protein L3, apicoplast, putative
Plasmodium vivax PVX_101165   50S ribosomal protein L3, putative
Plasmodium yoelii PY07001   ribosomal protein L3, putative
Plasmodium yoelii PY04814   ribosomal protein L3, putative
Saccharomyces cerevisiae YGR220C   mitochondrial 54S ribosomal protein YmL9
Schistosoma japonicum Sjp_0212870   ko:K02906 large subunit ribosomal protein L3, putative
Schistosoma mansoni Smp_087440   50S ribosomal protein L3
Schmidtea mediterranea mk4.000669.05   Putative 39S ribosomal protein L3, mitochondrial
Trypanosoma brucei gambiense Tbg972.3.6310   ribosomal protein L3 mitochondrial, putative
Trypanosoma brucei Tb927.3.5610   Mitochondrial ribosomal protein L3
Trypanosoma congolense TcIL3000_3_3550   ribosomal protein L3 mitochondrial, putative
Trypanosoma cruzi TcCLB.510645.49   ribosomal protein L3 mitochondrial, putative
Trypanosoma cruzi TcCLB.507795.100   mitochondrial ribosomal protein L3, putative
Toxoplasma gondii TGME49_230050   50S ribosomal protein L3, putative
Toxoplasma gondii TGME49_243480   50S ribosomal protein L3, putative
Treponema pallidum TP0189   50S ribosomal protein L3
Theileria parva TP03_0514   50S ribosomal protein L3, putative
Theileria parva TP04_0733   60S ribosomal protein L3, putative
Wolbachia endosymbiont of Brugia malayi Wbm0341   50S ribosomal protein L3

Essentiality

PF3D7_1245400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu713 Mycobacterium tuberculosis essential nmpdr
Tb927.3.5610 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.5610 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.5610 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.5610 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3320 Escherichia coli essential goodall
CELE_C26E6.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_C26E6.6 Caenorhabditis elegans larval arrest wormbase
CELE_C26E6.6 Caenorhabditis elegans slow growth wormbase
CELE_C26E6.6 Caenorhabditis elegans sterile wormbase
PBANKA_0819200 Plasmodium berghei Essential plasmo
PBANKA_1458600 Plasmodium berghei Essential plasmo
TGME49_230050 Toxoplasma gondii Probably essential sidik
TGME49_243480 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PF3D7_1245400 (Plasmodium falciparum), mitochondrial ribosomal protein L3 precursor, putative
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